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Could you be more informative with regard to which data you have and what you aim to obtain?
Hello, I have a lncRNA and know it's chromosome, genomic start and end coordinate. Right now, I am trying to extract all the known genes from UCSC,hg38.
Try to be as informative as possible when asking questions.
Can you clarify what you mean with an up and downstream gene? Is it in a pathway, functionally, or the genomic coordinates, the location?
UCSC has a table browser which should allow you to extract "the known genes".
Hello, I got some lncRNAs, ex. TP4 chr4 10001(start position) 101030(end position). I need to find all the genes that located within 2000 bp of lncRNA's upstream and downstream. Thank you.
I would use bedtools annotate or similar for this, make a bed file containing (for your example):
And annotate that with all genes